a*pa evals: update readme and makefile

evals/astarpa/README.md

@@ -2,7 +2,18 @@
 
 This directory contains the evals for the A\*PA paper.
 
-- `experiments/` contains the `.yaml` files with experiment configurations.
-- `evals.ipynb` contains all plots and other statistics presented in the paper.
-  Unzip `results.zip` (`make unzip_results`) to reproduce them on data from the paper.
-- `make run` is the entrypoint to rerun all experiments in the `experiments` directory.
+- `experiments/` contains `.yaml` files with experiment configurations, roughly
+  corresponding to the plots in the paper. (Some `.yaml` files are the source of
+  multiple plots.)
+- Use `make download_results` to download and extract the `results.zip` from the
+  [`astarpa-evals` release](https://github.com/pairwise-alignment/pa-bench/releases/tag/astarpa-evals) on github.
+- Alternatively, `make run` reruns all experiments locally, but be aware that
+  this takes a long time (1-2 days). You could make things faster by running
+  more in parallel (add e.g. `-j 5` to the `run` rule in `makefile`), or by
+  lowering the number of sequences tested (e.g. lower `total_size` in `experiments/*.yaml`).
+- `evals.ipynb` contains all plots and other statistics presented in the paper
+  from the `results/*.json` files generated by one of the two steps above. The
+  version in the repo should correspond to the latest executed version and include all plots.
+
+note: the git history of the `evals.ipynb` file has been squashed to reduce the
+size of the repo.

evals/astarpa/makefile

@@ -38,5 +38,10 @@ prep:
 
 zip_results:
 	zip results.zip results/*.json
-unzip_results:
+
+# Download the results from the github release and unzip them.
+# See readme for more.
+download_results:
+	wget 'https://github.com/pairwise-alignment/pa-bench/releases/download/astarpa-evals/results.zip'
 	unzip results.zip
+	rm results.zip